Orientation Module 1 | P a g e

Table of Contents

Getting Started ................................................................................................................ 2

System Requirements ................................................................................................. 3

Course Information ...................................................................................................... 4

Acknowledgements ......................................................................................................... 5

Course Overview............................................................................................................. 6

Course Objectives ....................................................................................................... 7

Emergency Support Function ...................................................................................... 8

Animal Health Incidents and Carcass Management .................................................... 9

Course Structure........................................................................................................ 10

Introduction Modules..................................................................................................... 11

Carcass Management Modules..................................................................................... 12

Carcass Management Options Matrix ........................................................................... 14

Large Animal Carcass Decision Loop........................................................................ 15

HPAI Carcass Decision Loop .................................................................................... 16

Costs of Carcass Management ..................................................................................... 17

Contracts ................................................................................................................... 18

Summary....................................................................................................................... 21
Orientation Module 2 | P a g e

Getting Started

Welcome to the Orientation Module of the online Carcass Management Course. This 

course will present a series of Introduction and Carcass Management Modules, which 

address carcass management planning and operations, during animal health

emergencies. 

Completion of the five modules in the Introduction Modules is recommended, before 

undertaking any of the seven Carcass Management Modules.
Orientation Module 3 | P a g e

System Requirements

You must have the following programs installed to fully access this course:

 Modern desktop browser such as Microsoft® Internet Explorer® 8 or higher, 

Google ®Chrome, or Mozilla® Firefox

 Adobe® Reader

The modules in the Carcass Management Course may be viewed in any order; 

however, completion of the entire Introduction Module Series is recommended before 

completing any of the Carcass Management Option Modules. 

 To exit a module before completion, simply close it

 If using AgLearn, its bookmarking feature provides the option for returning to the 

last-viewed page

 If the course is being viewed from a website or from a self-launching CD, 

bookmarking may not be available 

For questions concerning course content or to recommend changes to the course, 

please contact the Veterinary Services, Office of Science, Technology, and Analysis 

Services (STAS), Interagency Coordination at 301-851-3565.

If you have difficulties with AgLearn functionality, contact the AgLearn Help Desk at 

866-633-9394.
Orientation Module 4 | P a g e

Course Information

Target Audience: The target audience for this course includes: 

 Federal, State, & Local employees

 Animal health emergency responders 

 Academia & industry personnel

 Accredited veterinarians 

 Livestock and poultry operators 

 Contractors (e.g., equipment operators, truck drivers, laborers, etc.) 

Prerequisites: None 

Course completion: The Introduction Module series is followed by seven Carcass 

Management Modules. After finishing each training module, you can download a

Certificate of Completion.

Additional course information can be found by visiting the following sections: 

 Acronyms

 Definitions

 References
Orientation Module 5 | P a g e

Acknowledgements

These materials were updated by Cubic Global Defense with funding from the U.S. 

Department of Homeland Security Science and Technology Directorate (DHS S&T) and 

in collaboration with the United States Department of Agriculture (USDA) Animal and 

Plant Health Inspection Service (APHIS).

Development and preparation of the course is attributed to: 

DHS S&T:

Dr. Michelle M. Colby, DVM., MS

Agriculture Defense Branch Chief

Chemical and Biological Defense 

Division

Science and Technology Directorate

Department of Homeland Security

Phone: 202-254-6883

Email: michelle.colby@hq.dhs.gov

USDA APHIS:

Ms. Lori P. Miller, PE

Senior Staff Officer/Environmental 

Engineer

USDA APHIS Veterinary Services

Science, Technology and Analysis 

Services

4700 River Road, Unit 41, Room 5D03.2

Riverdale, MD 20737

Phone: 301-851-3512

Email: lori.p.miller@aphis.usda.gov

Cubic Global Defense | 2280 Historic Decatur Rd. Ste 200 San Diego, CA 92106

Phone: 858-810-5749

Ms. Stacey Tyler

Program Manager

Email: stacey.tyler@cubic.com

Mr. Frank Acosta

Task Lead

Email: frank.acosta@cubic.com

Ms. Emilie Hill

Email: emilie.hill@cubic.com

Mr. Wayne Einfeld

Email: wayne.einfeld@cubic.com

Mr. Tim McSherry 

Email: tim.mcsherry@cubic.com

Ms. Jane Chemodanova

Email: jane.chemodanova@cubic.com

Mr. Kevin Groves

Email: kevin.groves@cubic.com

DHS S&T and the USDA would like to thank the individuals identified in the 

Acknowledgments section, for their time and expertise in content development and 

content review.
Orientation Module 6 | P a g e

Course Overview

This course focuses on the responsibilities of carcass management personnel, 

evaluation of carcass management options, and selection and execution of optimal 

methods. 

During a foreign animal disease (FAD) outbreak, effective management of animal 

carcasses and materials is a key component of a successful response. Proper 

management can help prevent or mitigate the spread of pathogens. 

The goal of carcass management is to protect the agricultural and national economy 

through the control and containment of disease by conducting carcass management 

operations in a timely, safe, biosecure, aesthetically acceptable, and environmentally 

responsible manner. 

If any materials (for example, bedding or feed) are potentially contaminated, they must 

undergo treatment or other management method to inactivate or contain the infectious 

agent or pathogen. Wastes requiring management may include: carcasses; 

contaminated manure, litter, and bedding; contaminated feed; contaminated personal 

protection equipment (PPE); contaminated materials and equipment that cannot be 

cleaned and disinfected; as well as chemicals from cleaning and disinfecting. It is also 

possible that milk and milk products from a quarantined area will require management.
Orientation Module 7 | P a g e

Course Objectives

The objectives of the course are as follows:

 Studying the APHIS Animal Health Emergency Management Tools for choosing 

the appropriate carcass management options 

 Selecting health, safety, and personal protective equipment (PPE) measures 

necessary to reduce risk to human health and preventing the spread of harmful 

agents to other people or animals 

 Implementing Secure Transport guidelines for movement of large numbers of 

contaminated or infected carcasses to prevent undesired environmental impacts, 

public health risks, and disease spread 

 Determining risks and applying Biosecurity controls focused on movements of 

animals, personnel, and conveyances

 Reviewing Carcass Management methods and procedures and selecting the 

most suitable option, based on pertinent Federal, State, and Local restrictions 
Orientation Module 8 | P a g e

Emergency Support Function

The Emergency Support Functions (ESF) provide the structure for coordinating Federal 

interagency support for a Federal response to an incident, both for declared disasters 

and emergencies under the Stafford Act and for non-Stafford Act incidents. 

 ESF #11 is activated by the Secretary of Homeland Security if requested by the 

primary agencies

 The USDA and the U.S. Department of the Interior (DOI) are the primary 

agencies for ESF #11. USDA is the ESF #11 Coordinator and has delegated its 

coordinating role to APHIS. Figure 2 lists the key roles and responsibilities.

 The USDA Natural Resources Conservation Service (NRCS) may provide local 

assistance for carcass management under the Emergency Watershed Protection 

Program (EWPP), and may also provide private landowners with technical 

assistance for carcass management if requested following a natural disaster.

 The USDA Farm Service Agency (FSA) may provide assistance for farmland 

debris cleanup through the Emergency Conservation Program 

 If there is evidence that an animal was exposed to a pest or disease of livestock, 

USDA may exercise authority under the Animal Health Protection Act to destroy 

and dispose of the animal carcass

Figure 1. Local, State, & Federal Response Levels (Click to Enlarge Image)
Orientation Module 9 | P a g e

Animal Health Incidents and Carcass Management

Although this course focuses on carcass management, it is important to have an 

understanding of the entire depopulation, carcass management and decontamination

process during a response operation:

The general order of events is:

 Depopulation of animals, management of the waste materials including 

carcasses, and decontamination of facilities, equipment, personnel, and nondisposable supplies

 Once the site is released from quarantine, animal agriculture operations can 

resume 

Methodologies used in the various phases of the operation are interrelated. Therefore, it 

is important to coordinate activities and communicate with all teams involved to ensure 

the animal health emergency response operation goes as smoothly as possible.

Figure 2. 3D Operations 
Orientation Module 10 | P a g e

Course Structure

The Carcass Management Course contains five Introduction Modules and seven 

Carcass Management Modules. Below is the list of modules and the approximate 

amount of time needed to complete each one. 

Introduction Modules

1. Orientation Module: 30 minutes

2. Emergency Management Tools Module: 45 minutes

3. Health, Safety, and PPE Module: 1 hour

4. Secure Transport Module: 1 hour

5. Biosecurity Module: 1 hour

Carcass Management Modules

1. Off-site Permitted Landfill Module: 1 - 2 hours

2. Rendering Module: 1 hour

3. Off-site Incineration Module: 1 hour

4. Composting Module: 1- 2 hours

5. Open Burning Module: 1 hour

6. On-site Burial Module: 1 hour

7. Mobile Treatment Technologies Module: 1 -2 hours
Orientation Module 11 | P a g e

Introduction Modules

Orientation

This module is the first of a series of Introduction Modules to the Carcass Management 

Course. This module provides an overview of the set of modules comprising the course, 

and introduces the Carcass Management Options Matrix and the Carcass Management 

Decision Loops.

Emergency Management Tools 

This module familiarizes responders with key decision making tools for use during an 

animal health emergency. This module introduces a suite of tools and emphasizes the 

importance of building a carcass management plan. A Site Specific Carcass 

Management Plan template is also provided in the module.

Health, Safety, and PPE

This module highlights the risk to human health and recommends mitigations for 

preventing human exposure to contaminants during carcass management operations. 

Responders must take the appropriate precautions to protect themselves from exposure 

to harmful agents, and they must ensure that they do not spread the hazard to other 

people or animals.

Secure Transport

This module discusses the safe and secure transportation of large numbers of 

contaminated or infected livestock carcasses. This activity requires significant planning 

and preparation to prevent undesired environmental impacts; public health risks, and 

further disease spread through diseased animal transport. 

Biosecurity

This module describes the biosecurity procedures needed to prevent the spread of 

disease. When properly implemented, these measures help reduce the risk of pathogen 

transmission during the movement of personnel and material necessary for the 

extensive activities of an incident response, such as carcass management. 
Orientation Module 12 | P a g e

Carcass Management Modules

Seven carcass management options are presented in the course. 

Off-site Permitted Landfill 

This module addresses the use of off-site permitted landfills which are engineered 

structures built into or on top of the ground in order to isolate waste from the 

environment (groundwater, air, rain). Landfills differ from "dumps" in that they have a

liner (usually clay or plastic) to keep the waste from polluting the surrounding area. 

Rendering

This module addresses rendering which uses heat and pressure to convert carcasses 

into protein-based solids, water, and tallow. Rendering plants may be either integrated 

with existing packing or processing plants or independent, receiving animal carcasses 

from farms and ranches.

Off-site Incineration 

This module addresses off-site incineration, which involves securely transporting 

carcasses to a fixed incineration facility, such as incinerators dedicated to: municipal 

waste, medical infectious waste, hazardous waste or pathological waste. Incinerators

consist of a hearth where waste materials are combusted at high temperatures, 

resulting in ash. Fixed incinerators have air emissions control devices to reduce 

pollution. 
Orientation Module 13 | P a g e

Carcass Management Modules (cont.)

Composting

This module describes composting as a carcass management method that promotes 

biomass decomposition through placement of carcasses between layers of carbon rich 

organic materials. The decomposition process requires a prescribed level of nitrogen, 

carbon, oxygen, and moisture for optimal tissue breakdown. In the composting process, 

carcasses serve as the source of nitrogen, while the addition of high carbon plant 

material meets the carbon requirement. 

Open Burning 

This module addresses open-air burning, which involves combustion of waste at high 

temperatures, converting it into heat, gaseous emissions, and ash. Open-air burning 

may be accomplished by burning on open land at an above-ground site, in a dug-out pit, 

or on combustible heaps called pyres. Open-air burning operations are strictly regulated

by State or Local officials. 

On-site Burial 

This module explains the use of on-site burial which can include lined and unlined 

trench or pit methods. The two on-site carcass management methods covered in this 

module include unlined trenches and lined burial sites. 

Mobile Treatment Technologies 

This module describes several mobile treatment technologies which can be delivered to 

the infected premises and treat the carcasses on-site avoiding the risk from transport.

The ones mentioned in this module include: Mobile Incineration, Mobile Autoclave 

Shredding and Mobile Alkaline Hydrolysis. 
Orientation Module 14 | P a g e

Carcass Management Options Matrix

USDA APHIS has developed emergency management tools to be utilized during an 

animal health emergency. The tools have been grouped together into a single Matrix, 

Decision Loop, and Checklist (MLCh Tool).

The first component of the MLCh Tool is the Carcass Management Options Matrix that 

ranks the major carcass management options based on 15 different criteria. A more 

detailed explanation of the Matrix is found in the Emergency Management Tools 

Module.

Figure 3. Carcass Management Options Matrix (Click on the Image to Enlarge It)
Orientation Module 15 | P a g e

Large Animal Carcass Decision Loop 

The second component of the MLCh Tool is the Carcass Management Decision Loop. 

 This series of questions is arranged in order of preference based on the Matrix

 The first decision loop shown applies primarily to a large animal disease outbreak

and follows the same order of preference as the matrix

 The second decision loop applies to Highly Pathogenic Avian Influenza (HPAI)

infected poultry

Figure 4. Large Animal Decision Loop (Click on the Image to Enlarge It)
Orientation Module 16 | P a g e

HPAI Carcass Decision Loop 

The HPAI loop begins with onsite options which are preferred for disease containment 

and are more feasible for poultry than for large animals due to the small size of the 

birds. 

Figure 5. HPAI Management Decision Loop (Click on the Image to Enlarge It)

A detailed explanation of the Decision Loops and Options Checklist can be found in the 

Emergency Management Tools Module.
Orientation Module 17 | P a g e

Costs of Carcass Management 

The cost of the various carcass management options are a factor in choosing from 

among the various alternatives. The management of large numbers of animal carcasses 

must be cost effective and protective of human health and the environment. 

 Contingency plans must consider the economic costs and the availability of 

resources for the actual carcass management/treatment, as well as numerous 

related costs

 In 2001, cost estimates for large-scale management of animal carcasses in the 

United Kingdom exceeded $400 million (McClaskey, 2004)

 In the 2002 avian influenza outbreaks in Virginia, costs for carcass management 

were estimated at $149 million

 Since the 1920s, the 10 multi-flock outbreaks of bird flu in the US cost the poultry 

industry $368 million, which does not include increased egg and poultry prices 

(Pepin et al., 2014)

 The 2014/2015 HPAI outbreak in the US cost the federal government 

approximately $171M for carcass management alone

Additional information can be found in the USDA, Carcass Management during a Mass 

Animal Health Emergency, Final Programmatic Environmental Impact Statement, 

December 2015.
Orientation Module 18 | P a g e

Contracts

In an emergency, the incident command team identifies a need for depopulation 

activities, or carcass management by hauling waste, for example. That need may be 

satisfied through several different means:

 First, with existing personnel and resources (using stockpile materials for 

example), or

 Second, through agreements with producers or other entities, or

 Finally, through use of contracts.

Contracts can be for goods, services, or some combination of both. This process is 

governed by Federal Acquisition Regulations (FAR), the Agricultural FAR Supplement 

(AGAR), Appropriations Law, and Dept. of Agriculture Directives and Procurement 

Advisories.

 Regulations require that procedures be followed that allow for maximum 

competition and transparency in government contracting

 A competitive process based on principles of fairness and transparency provides 

vendors with notice, information, and opportunities

 Solicitations are posted on the fbo.gov website, allow time for vendors to submit 

quotes, and evaluate proposals based on criteria established in the solicitation
Orientation Module 19 | P a g e

Contracts (cont.)

To use contracting as a means to obtain goods and services, the command team must 

submit a requisition package to the Procurement branch. That requisition package must 

contain funding, a description of the requirement (often called a Statement of Work), 

any known sources, a technical point of contact (POC) and any required justifications.

 One justification that is often used in an emergency is Unusual and Compelling 

Urgency (FAR 6.302-2)

 This authority allows “When the agency’s need for the supplies or services is of 

such an unusual and compelling urgency that the Government would be 

seriously injured unless the agency is permitted to limit the number of sources 

from which it solicits bids or proposals, full and open competition need not be 

provided for.”

 This justification allows the government to use a different procedure in an 

emergency to save time

The contracting officer will use the information submitted by the command team to 

create a solicitation.

 The solicitation will be sent to a vendor (or vendors depending on the situation)

 Vendors will submit a price and a proposal and the information will then be 

evaluated by the contracting officer and the technical POC

 The process may or may not include negotiation. Vendors may also be asked for 

past performance and capability information. 
Orientation Module 20 | P a g e

Contracts (cont.)

Only warranted contracting officers have the authority to enter into contracts and to 

make changes in contracts. When an individual or government employee enters into a 

contract or directs the performance of a vendor without the authority to do so, it creates 

an unauthorized commitment.

 Employees can then be held financially responsible for these commitments 

unless a ratification is obtained

 A ratification occurs when the Government agrees to pay for the unauthorized 

commitment

 Ratifications can only be approved by high level APHIS officials under certain 

circumstances (FAR 1.602-3)

As part of its ongoing mission, APHIS Veterinary Services stockpiles supplies. 

Contracting for supplies for the stockpile is ongoing and as supplies are used, they are 

replenished.

The Government is limited in its ability to contract ahead of time for an emergency. 

Appropriations law principles prevent contracting when a need does not yet exist. In 

addition, it may not be practicable to contract for services, before knowing when or 

where they might be needed.
Orientation Module 21 | P a g e

Summary

You have completed the Orientation Module of the Introduction Modules. In this module, 

you have been introduced to:

 The carcass management course overview and objectives

 The emergency response process during a 3D operation

 The Introduction Modules 

 The Carcass Management Modules

 The Carcass Management Matrix, Decision Loops, and Checklist (MLCh) tool

Return to the Home Page and begin the next module, Emergency Management Tools.